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Makhatadze GI, Chen CR, Khutsishvili I, Marky LA. The volume changes of unfolding of dsDNA. Biophys J 2022; 121:4892-4899. [PMID: 35962547 PMCID: PMC9811605 DOI: 10.1016/j.bpj.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/07/2023] Open
Abstract
High hydrostatic pressure can have profound effects on the stability of biomacromolecules. The magnitude and direction (stabilizing or destabilizing) of this effect is defined by the volume changes in the system, ΔV. Positive volume changes will stabilize the starting native state, whereas negative volume changes will lead to the stabilization of the final unfolded state. For the DNA double helix, experimental data suggested that when the thermostability of dsDNA is below 50°C, increase in hydrostatic pressure will lead to destabilization; i.e., helix-to-coil transition has negative ΔV. In contrast, the dsDNA sequences with the thermostability above 50°C showed positive ΔV values and were stabilized by hydrostatic pressure. In order to get insight into this switch in the response of dsDNA to hydrostatic pressure as a function of temperature, first we further validated this trend using experimental measurements of ΔV for 10 different dsDNA sequences using pressure perturbation calorimetry. We also developed a computational protocol to calculate the expected volume changes of dsDNA unfolding, which was benchmarked against the experimental set of 50 ΔV values that included, in addition to our data, the values from the literature. Computation predicts well the experimental values of ΔV. Such agreement between computation and experiment lends credibility to the computation protocol and provides molecular level rational for the observed temperature dependence of ΔV that can be traced to the hydration. Difference in the ΔV value for A/T versus G/C basepairs is also discussed.
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Affiliation(s)
- George I Makhatadze
- Departments of Biological Sciences, Chemistry, and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.
| | - Calvin R Chen
- Departments of Biological Sciences, Chemistry, and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska
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Hu X, Li F, Noor N, Ling D. Platinum drugs: from Pt(II) compounds, Pt(IV) prodrugs, to Pt nanocrystals/nanoclusters. Sci Bull (Beijing) 2017; 62:589-596. [PMID: 36659367 DOI: 10.1016/j.scib.2017.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 01/21/2023]
Abstract
Platinum (Pt) based drugs, such as cisplatin, are widely used as anti-cancer agents, but their severe adverse reactions and resistance of cancer patients have limited their board clinical use. For the last few decades, Pt(II) compounds, Pt(IV) prodrugs as well as smart drug delivery systems have been developed to overcome these problems. However, most conventional strategies rely on the similar anti-cancer mechanism with cisplatin and consequently only achieve limited success. Recently, Pt nanocrystals/nanoclusters (Pt NCs), with a brand new anti-cancer mechanism, have shown a promising potential in targeted cancer therapy, especially in Pt resistance circumvention. This review is helpful to understand the research strategies of Pt drugs, particularly, the recent developments and medical applications of Pt NCs.
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Affiliation(s)
- Xi Hu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fangyuan Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Nabila Noor
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Daishun Ling
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China.
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Lando DY, Chang CL, Fridman AS, Grigoryan IE, Galyuk EN, Hsueh YW, Hu CK. Comparative thermal and thermodynamic study of DNA chemically modified with antitumor drug cisplatin and its inactive analog transplatin. J Inorg Biochem 2014; 137:85-93. [PMID: 24831492 DOI: 10.1016/j.jinorgbio.2014.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 12/11/2022]
Abstract
Antitumor activity of cisplatin is exerted by covalent binding to DNA. For comparison, studies of cisplatin-DNA complexes often employ the very similar but inactive transplatin. In this work, thermal and thermodynamic properties of DNA complexes with these compounds were studied using differential scanning calorimetry (DSC) and computer modeling. DSC demonstrates that cisplatin decreases thermal stability (melting temperature, Tm) of long DNA, and transplatin increases it. At the same time, both compounds decrease the enthalpy and entropy of the helix-coil transition, and the impact of transplatin is much higher. From Pt/nucleotide molar ratio rb=0.001, both compounds destroy the fine structure of DSC profile and increase the temperature melting range (ΔT). For cisplatin and transplatin, the dependences δTm vs rb differ in sign, while δΔT vs rb are positive for both compounds. The change in the parameter δΔT vs rb demonstrates the GC specificity in the location of DNA distortions. Our experimental results and calculations show that 1) in contrast to [Pt(dien)Cl]Cl, monofunctional adducts formed by transplatin decrease the thermal stability of long DNA at [Na(+)]>30mM; 2) interstrand crosslinks of cisplatin and transplatin only slightly increase Tm; 3) the difference in thermal stability of DNA complexes with cisplatin vs DNA complexes with transplatin mainly arises from the different thermodynamic properties of their intrastrand crosslinks. This type of crosslink appears to be responsible for the antitumor activity of cisplatin. At any [Na(+)] from interval 10-210mM, cisplatin and transplatin intrastrand crosslinks give rise to destabilization and stabilization, respectively.
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Affiliation(s)
- Dmitri Y Lando
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus.
| | - Chun-Ling Chang
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Alexander S Fridman
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | | | - Elena N Galyuk
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Ya-Wei Hsueh
- Department of Physics, National Central University, Chungli 32001, Taiwan
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan.
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Polonyi C, Albertsson I, Damian MS, Elmroth SKC. Comparison of Cis- and Oxaliplatin-induced Destabilization of 15-mer DNA- and RNA Duplexes by Binding to Centrally Located GG- and GNG Sequences. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Khutsishvili I, Zhang N, Marky LA, Crean C, Patel DJ, Geacintov NE, Shafirovich V. Thermodynamic profiles and nuclear magnetic resonance studies of oligonucleotide duplexes containing single diastereomeric spiroiminodihydantoin lesions. Biochemistry 2013; 52:1354-63. [PMID: 23360616 DOI: 10.1021/bi301566v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spiroiminodihydantoins (Sp) are highly mutagenic oxidation products of guanine and 8-oxo-7,8-dihydroguanine in DNA. The Sp lesions have recently been detected in the liver and colon of mice infected with Helicobacter hepaticus that induces inflammation and the development of liver and colon cancers in murine model systems [Mangerich, A., et al. (2012) Proc. Natl. Acad. Sci. U.S.A. 109, E1820-E1829]. The impact of Sp lesions on the thermodynamic characteristics and the effects of the diastereomeric Sp-R and Sp-S lesions on the conformational features of double-stranded 11-mer oligonucleotide duplexes have been studied by a combination of microcalorimetric methods, analysis of DNA melting curves, and two-dimensional nuclear magnetic resonance methods. The nonplanar, propeller-like shapes of the Sp residues strongly diminish the extent of local base stacking interactions that destabilize the DNA duplexes characterized by unfavorable enthalpy contributions. Relative to that of an unmodified duplex, the thermally induced unfolding of the duplexes with centrally positioned Sp-R and Sp-S lesions into single strands is accompanied by a smaller release of cationic counterions (Δn(Na⁺) = 0.6 mol of Na⁺/mol of duplex) and water molecules (Δn(w) = 17 mol of H₂O/mol of duplex). The unfolding parameters are similar for the Sp-R and Sp-S lesions, although their orientations in the duplexes are different. The structural disturbances radiate one base pair beyond the flanking C:G pair, although Watson-Crick hydrogen bonding is maintained at all flanking base pairs. The observed relatively strong destabilization of B-form DNA by the physically small Sp lesions is expected to have a significant impact on the processing of these lesions in biological environments.
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Affiliation(s)
- Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-4628, United States
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Lando DY, Galyuk EN, Chang CL, Hu CK. Temporal behavior of DNA thermal stability in the presence of platinum compounds. Role of monofunctional and bifunctional adducts. J Inorg Biochem 2012; 117:164-70. [DOI: 10.1016/j.jinorgbio.2012.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/24/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
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Snygg ÅS, Elmroth SK. Expanding the chemical nature of siRNAs: Oxaliplatin as metalation reagent. Biochem Biophys Res Commun 2009; 379:186-90. [DOI: 10.1016/j.bbrc.2008.12.068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 12/04/2008] [Indexed: 01/24/2023]
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Galyuk EN, Fridman AS, Vorobev VI, Haroutiunian SG, Sargsyan SA, Hauruk MM, Lando DY. Compensation of DNA Stabilization and Destabilization Effects Caused by Cisplatin is Partially Disturbed in Alkaline Medium. J Biomol Struct Dyn 2008; 25:407-17. [DOI: 10.1080/07391102.2008.10507189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Srivastava S, Srivastava S, Gupta VD, Prakash Gupta V. Impact ofcis/trans‐Platin Binding on DNA Stability. J MACROMOL SCI B 2007. [DOI: 10.1081/mb-120030025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shinoo Srivastava
- a Physics Department , Lucknow University , Lucknow , 226 007 , India
| | - Seema Srivastava
- a Physics Department , Lucknow University , Lucknow , 226 007 , India
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Abstract
The ligand-loss photochemistry of cis-[Ru(bpy)(2)(NH(3))(2)](2+) (bpy = 2,2'-bipyridine) was investigated in water and in the presence of added ligands such as bipyridine and chloride. Irradiation of the complex results in the covalent binding to 9-methyl- and 9-ethylguanine, as well as to single-stranded and double-stranded DNA. This photoinduced DNA binding is not observed for the control complex [Ru(bpy)(2)(en)](2+) (en = ethylenediamine) under similar irradiation conditions. The results presented here show that octahedral Ru(II) complexes with photolabile ligands may prove useful as photoactivated cisplatin analogs.
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Affiliation(s)
- Tanya N Singh
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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